2qfd

Crystal structure of the regulatory domain of human RIG-I with bound Hg

Method: X-RAY DIFFRACTION D_max: 131.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable ATP-dependent RNA helicase DDX58

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 802–925	Fragment：Regulatory domain	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.70 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2QFD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LWD Solution structure of second CARD of human RIG-I Deposited 2012-07-27	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 95–190（96 aa） Fragment：CARD 2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 300 uM [U-100% 15N] card2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 100% D2O \| 100% D2O	Resolution not provided
2LWE Solution structure of mutant (T170E) second CARD of human RIG-I Deposited 2012-07-27	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 95–190（96 aa） Fragment：CARD 2 domain	Mutation：T170E	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 300 uM [U-100% 15N] card2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 300 uM [U-100% 13C; U-100% 15N] card2, 100% D2O \| 100% D2O	Resolution not provided
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2QFB Crystal structure of the regulatory domain of human RIG-I with bound Zn Deposited 2007-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 802–925（124 aa） Fragment：Regulatory domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10；293.15 K；0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.00 Å R-free 0.285
2RMJ Solution structure of RIG-I C-terminal domain Deposited 2007-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–925（134 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 0.25 NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] RIG-I, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YKG Structural insights into RNA recognition by RIG-I Deposited 2011-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 230–925（696 aa） Fragment：RESIDUES 230-925	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；0.1 M BICINE, PH 9.0, 22.5 % POLYETHYLENE GLYCOL 6,000	Resolution 2.50 Å R-free 0.273
3LRN Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA Deposited 2010-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 803–923（121 aa） Fragment：human RIG-I CTD Chain B 803–923（121 aa） Fragment：human RIG-I CTD	Mutation：C829S Mutation：C829S	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；15% PEG 3,350, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.282
3LRR Crystal structure of human RIG-I CTD bound to a 12 bp AU rich 5' ppp dsRNA Deposited 2010-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 803–923（121 aa） Fragment：RIG-I CTD (UNP residues 803 to 923) Chain B 803–923（121 aa） Fragment：RIG-I CTD (UNP residues 803 to 923)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 3,350 (15%) plus ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.15 Å R-free 0.228
3NCU Structural and functional insights into pattern recognition by the innate immune receptor RIG-I Deposited 2010-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 792–925（134 aa） Fragment：residues 792-925 Chain B 792–925（134 aa） Fragment：residues 792-925	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；27% (v/v) polyethylene glycerol 3350 (PEG 3350), 50 mM Tris-HCl, pH 7.5, 0.1 M KCl, and 10 mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.55 Å R-free 0.229
3OG8 Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA Deposited 2010-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 802–925（124 aa） Fragment：C-terminal domain Chain B 802–925（124 aa） Fragment：C-terminal domain	Mutation：C829S Mutation：C829S	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；27% PEG MME 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.278
3ZD6 Snapshot 1 of RIG-I scanning on RNA duplex Deposited 2012-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 185–880（696 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9	Resolution 2.80 Å R-free 0.279
3ZD7 Snapshot 3 of RIG-I scanning on RNA duplex Deposited 2012-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 185–880（696 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9	Resolution 2.50 Å R-free 0.288
4AY2 Capturing 5' tri-phosphorylated RNA duplex by RIG-I Deposited 2012-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 239–925（687 aa） Fragment：RESIDUES 239-925	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.286
4BPB STRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I Deposited 2013-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 230–925（696 aa） Fragment：RESIDUES 230-925	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；0.1 M BICINE, PH 9.0, 22.5 % POLYETHYLENE GLYCOL 6,000	Resolution 2.58 Å R-free 0.255
4NQK Structure of an Ubiquitin complex Deposited 2013-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200 Chain B 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200 Chain C 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200 Chain D 1–200（200 aa） Fragment：N-terminal tandem CARD domain, UNP residues 1-200	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22% PEG3350, 0.2 M Tri-Li Citrate, 3% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.70 Å R-free 0.285
4ON9 DECH box helicase domain Deposited 2014-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 230–793（564 aa） Fragment：UNP residues 230-793	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.71 Å R-free 0.258
4ON9 DECH box helicase domain Deposited 2014-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 230–793（564 aa） Fragment：UNP residues 230-793	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.71 Å R-free 0.258
4ON9 DECH box helicase domain Deposited 2014-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 230–793（564 aa） Fragment：UNP residues 230-793 Chain B 230–793（564 aa） Fragment：UNP residues 230-793	Not recorded	SO4 SULFATE ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；288 K；1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.71 Å R-free 0.258
4P4H Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain Deposited 2014-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 1–201（201 aa） Chain B 1–201（201 aa） Chain C 1–201（201 aa） Chain D 1–201（201 aa） Chain E 1–201（201 aa） Chain F 1–201（201 aa） Chain G 1–201（201 aa） Chain H 1–201（201 aa）	Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A Mutation：E52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Tri-Li Citrate, PEG 3350, Cr(III) Cl3	Resolution 3.40 Å R-free 0.240
5E3H Structural Basis for RNA Recognition and Activation of RIG-I Deposited 2015-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 232–925（694 aa） Fragment：UNP residues 232-925	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% w/v PEG3350, 0.25 M sodium thiocyanate, 100 mM MOPS, pH 7.8, 3% v/v 2,2,2-trifluoroethanol	Resolution 2.70 Å R-free 0.268
5F98 Crystal structure of RIG-I in complex with Cap-0 RNA Deposited 2015-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: dodecameric	Chain A 232–925（694 aa） Chain C 232–925（694 aa） Chain E 232–925（694 aa） Chain G 232–925（694 aa） Chain I 232–925（694 aa） Chain K 232–925（694 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6 M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；20% (w/v) PEG 3350, 0.2 M NaSCN, 100 mM MOPS (pH 7.8), 3.5% (v/v) 2,2,2-trifluoroethanol	Resolution 3.28 Å R-free 0.277
5F9F Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA Deposited 2015-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: dodecameric	Chain A 187–880（694 aa） Chain C 187–880（694 aa） Chain E 187–880（694 aa） Chain G 187–880（694 aa） Chain I 187–880（694 aa） Chain K 187–880（694 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 6 ETF TRIFLUOROETHANOL × 4 BU3 (R,R)-2,3-BUTANEDIOL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；23% (w/v) PEG 3350, 0.3 M NaSCN, 100 mM MOPS (pH 7.8)	Resolution 2.60 Å R-free 0.259
5F9H Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA Deposited 2015-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: dodecameric	Chain A 232–925（694 aa） Chain C 232–925（694 aa） Chain E 232–925（694 aa） Chain G 232–925（694 aa） Chain I 232–925（694 aa） Chain K 232–925（694 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；23% (w/v) PEG 3350, 0.25 M KSCN, 100 mM MOPS (pH 7.8)	Resolution 3.10 Å R-free 0.266
6GPG Structure of the RIG-I Singleton-Merten syndrome variant C268F Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 232–925（694 aa）	Mutation：C268F	ZN ZINC ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M MOPS pH 7.5, 17.5 % (w/v) PEG 3350, 0.25 M NaSCN, 3 % (v/v) 2,2,2 trifluoroethanol	Resolution 2.89 Å R-free 0.260
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 242–922（681 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic	Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain D 242–922（681 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic	Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain F 242–922（681 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic	Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain H 242–922（681 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic	Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain J 242–922（681 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic	Resolution 3.00 Å R-free 0.274
6KYV Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs Deposited 2019-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain L 242–922（681 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic	Resolution 3.00 Å R-free 0.274
7BAH Structure of RIG-I CTD bound to OH-RNA Deposited 2020-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 802–925（124 aa） Chain B 802–925（124 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；283.15 K；0.1 M Tris-HCl pH 8.0 0.2 M NaCl 18% PEG 3350	Resolution 1.89 Å R-free 0.224
7BAI Structure of RIG-I CTD (I875A) bound to p-RNA Deposited 2020-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 802–925（124 aa） Chain B 802–925（124 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.2 M thiocyanate pH 8.4 20% PEG 3350 10% ethylene glycol 10% MPD	Resolution 3.40 Å R-free 0.273
7BAI Structure of RIG-I CTD (I875A) bound to p-RNA Deposited 2020-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain E 802–925（124 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；0.2 M thiocyanate pH 8.4 20% PEG 3350 10% ethylene glycol 10% MPD	Resolution 3.40 Å R-free 0.273
7JL1 Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer) Deposited 2020-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 159–880（722 aa） Fragment：UNP residues 159-880	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7JL3 Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer) Deposited 2020-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 159–880（722 aa） Fragment：UNP residues 159-880 Chain C 159–880（722 aa） Fragment：UNP residues 159-880 Chain E 159–880（722 aa） Fragment：UNP residues 159-880	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ALF TETRAFLUOROALUMINATE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7MK1 Structure of a protein-modified aptamer complex Deposited 2021-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 801–925（125 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285.15 K；30% PEG3350, 0.01 M Na acetate pH 4.8	Resolution 1.90 Å R-free 0.220
7MK1 Structure of a protein-modified aptamer complex Deposited 2021-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 801–925（125 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285.15 K；30% PEG3350, 0.01 M Na acetate pH 4.8	Resolution 1.90 Å R-free 0.220
7TNX Cryo-EM structure of RIG-I in complex with p3dsRNA Deposited 2022-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
7TNY Cryo-EM structure of RIG-I in complex with p2dsRNA Deposited 2022-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7TNZ Cryo-EM structure of RIG-I in complex with p1dsRNA Deposited 2022-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
7TO0 Cryo-EM structure of RIG-I in complex with OHdsRNA Deposited 2022-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7TO1 Cryo-EM structure of RIG-I bound to the end of p3SLR30 (+ATP) Deposited 2022-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.66 Å
7TO2 Cryo-EM structure of RIG-I bound to the internal sites of p3SLR30 (+ATP) Deposited 2022-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8DVR Cryo-EM structure of RIG-I bound to the end of p3SLR30 (+AMPPNP) Deposited 2022-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8DVS Cryo-EM structure of RIG-I bound to the end of OHSLR30 (+ATP) Deposited 2022-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8DVU Cryo-EM structure of RIG-I bound to the internal sites of OHSLR30 (+ATP) Deposited 2022-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8G7T Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-end) Deposited 2023-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–925（925 aa） Chain C 1–925（925 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8G7U Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-semi-closed end) Deposited 2023-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–925（925 aa） Chain C 1–925（925 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8G7V Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-inter) Deposited 2023-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–925（925 aa） Chain C 1–925（925 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8SCZ Cryo-EM structure of 14aa-GS RIG-I in complex with p3SLR30 Deposited 2023-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8SD0 Cryo-EM structure of RIG-I in complex with p3SLR14 Deposited 2023-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9KTW Cryo-EM structure of wild type RIG-I with 5'p-RNA Deposited 2024-12-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–925（925 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25mM HEPES, 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9KU4 Cryo-EM structure of E373A mutant RIG-I with 5'p-RNA Deposited 2024-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–925（925 aa）	Mutation：E373A	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25mM HEPES, 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å

43 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DDX58_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–145； UniProt 802–925 Author chain B； PDBConstruct 22–145； UniProt 802–925 Author chain C； PDBConstruct 22–145； UniProt 802–925 Author chain D； PDBConstruct 22–145； UniProt 802–925 Author chain E； PDBConstruct 22–145； UniProt 802–925 Author chain F； PDBConstruct 22–145； UniProt 802–925 Author chain G； PDBConstruct 22–145； UniProt 802–925 Author chain H； PDBConstruct 22–145； UniProt 802–925 Author chain I； PDBConstruct 22–145； UniProt 802–925 Author chain J； PDBConstruct 22–145； UniProt 802–925

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2qfd
Deposition date deposition_date	2007-06-27
Structure title title	Crystal structure of the regulatory domain of human RIG-I with bound Hg
Keywords keywords	;Zinc Finger, Alternative splicing, Antiviral defense, ATP-binding, Helicase, Hydrolase, Immune response, Innate immunity, Interferon induction, Nucleotide-binding, Polymorphism, RNA-binding, Ubl conjugation ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.83 Å
Radius of gyration Rg (electron density) rg_electron	43.33 Å
Forward intensity I(0) i0	300963000.00
Molecular weight molecular_weight	143820.0 kDa
Excluded volume excluded_volume	180100 Å³
Envelope volume envelope_volume	279200 Å³
Hydration-shell volume shell_volume	54239 Å³
Envelope diameter envelope_diameter	138.6 Å
Shell Rg shell_rg	48.95 Å
Envelope Rg envelope_rg	41.09 Å
Shape Rg shape_rg	43.32 Å
Total Rg total_rg	43.67 Å
Total atoms total_atoms	9990
Residues n_residues	1210
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	131.5 Å
Rg (real space) rg_real	43.67 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	3.0100e+08
I(0) uncertainty (real space) i0_real_error	5.0270e+06
Rg (reciprocal space) rg_reciprocal	43.82 Å
I(0) (reciprocal space) i0_reciprocal	301000000.0000
Solution quality estimate total_estimate	0.8829
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.4 Å
Skewness Skewness skewness	0.054
Kurtosis Kurtosis kurtosis	-0.724
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14580000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.989; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.507

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Probable ATP-dependent RNA helicase DDX58
Molecular weight formula_weight	16853.5 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	10092

MGSSHHHHHHSSGLVPRGSHMDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2qfda_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdb_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdc_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdd_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfde_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdf_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdg_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdh_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdi_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2qfdj_
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

CATH v4.4 (10 domains)

Domain ID domain_id	2qfdA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdC00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdD00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdE00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdF00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdG00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdH00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdI00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

Domain ID domain_id	2qfdJ00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

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8. Citations (1)

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Unit-cell length a length_a	97.150 Å
Unit-cell length b length_b	76.540 Å
Unit-cell length c length_c	137.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2530
R_work r_work	0.2410
R_free r_free	0.2760

fit	/app/data/saxs_computation/qf/2qfd/2qfd.fit
pddf	/app/data/pr_computation/qf/2qfd/2qfd.pr.out
profile	/app/data/saxs_computation/qf/2qfd/2qfd.dat